July 2024 Newsletter
Our July software updates include nine new and updated titles for Mac and Linux. New software titles can be requested by sending email to help@biogrids.org or filling out our Software Request Form.
Remote Working Help
The BioGrids Wiki provides step by step instructions for installing BioGrids software on a local laptop or desktop machine. If you prefer a live demonstration, or run into trouble, please contact help@biogrids.org. We can set up a Zoom meeting to assist you.
Cite BioGrids
If your use of BioGrids supplied software was an important element in your publication, please include the following statement in your work:
"Software used in the project was installed and configured by BioGrids
(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"
See our Grant Support page for additional details.
Register here to try out our software installer, which allows users to choose from over 660 bioinformatics and life sciences tools that can be installed as ready-to-run applications on Mac or Linux machines with the click of a button or a short command from the CLI. No need to worry about dependencies or compilation.
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members. This includes all aspects of software installation and management. If you need assistance of any kind please send a note to: help@biogrids.org.
BioGrids Quickstart
The latest version of the BioGrids Installation Manager is available for Linux and MacOS computers from the BioGrids Wiki QuickStart page.
Start the BioGrids environment:
source /programs/biogrids.shrc
List available titles (Linux):
cat /programs/x86_64-linux/biogrids_x86_64-linux
List available titles (Mac):
cat /programs/i386-mac/biogrids_i386-mac
Get version and override info:
biogrids-info -l star
Get list of executables for a title:
biogrids-list star
Need more help? Send mail to: help@biogrids.org
Software Updates
mhcflurry - MHC I ligand prediction package with competitive accuracy and a fast and documented implementation.
Updated versions:2.1.2 | OS X INTEL 2.1.2 | Linux 64
Connectome Workbench - an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.
Updated versions:2.0.0 | Linux 64
Clair3 - a tool for symphonizing pileup and full-alignment for high-performance long-read variant calling
Updated versions:1.0.10 | Linux 64
Blender - a 3D creation suite that supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking.
Updated versions:4.2.0_x64 | OS X INTEL 4.1.1_x64 | OS X INTEL 4.1.1_arm64 | OS X INTEL 4.2.0_arm64 | OS X INTEL 4.1.1 | Linux 64 4.2.0 | Linux 64
ParaView - the world’s leading open source post-processing visualization engine.
Updated versions:5.12.1 | Linux 64 | OS X INTEL 5.12.1 | OS X INTEL
SQLite - a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine.
Updated versions:3.46.0 | OS X INTEL 3.46.0 | Linux 64
pySCENIC - a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
Updated versions:0.12.1 | OS X INTEL 0.11.2 | OS X INTEL 0.12.1 | Linux 64
Cell Ranger - a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Updated versions:8.0.1 | Linux 64
Metaphor - Metagenomic Pipeline for Short Reads
Updated versions:1.7.13 | Linux 64 1.7.13 | OS X INTEL
Software Training
Center for Computational Biomedicine
The Center for Computational Biomedicine (CCB) Fall newsletter contains training and collaboration opportunities.
HMS Research Computing
HMS Research Computing User Training
Bioinformatics Support
Need help getting software installed on new machines? Have you been planning to try Amazon Web Services (AWS) cloud computing?
BioGrids can help you get started. We have expertise in bioinformatics, programming, workflow development and high performance computing.
We improve the collection with feedback from the community.
Want to see a new application in BioGrids?
Let us know: help@biogrids.org
BioGrids is supported by Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SBGrid.
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